title: Standard biological parts knowledgebase.
abstract: We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.
authors.affiliation: Biomedical & Health Informatics, University of Washington, Seattle, Washington, United States of America.
authors.forename: Michal
authors.initials: M
authors.lastname: Galdzicki
authors.forename: Cesar
authors.initials: C
authors.lastname: Rodriguez
authors.forename: Deepak
authors.initials: D
authors.lastname: Chandran
authors.forename: Herbert M
authors.initials: HM
authors.lastname: Sauro
authors.forename: John H
authors.initials: JH
authors.lastname: Gennari
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence / Q000235:genetics; D001695:Biology / Q000379:methods / Q000592:standards*; D019295:Computational Biology / Q000379:methods / Q000592:standards; D003628:Database Management Systems / Q000592:standards; D016208:Databases, Factual / Q000592:standards*; D005818:Genetic Engineering / Q000379:methods / Q000592:standards; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D051188:Knowledge Bases; D008954:Models, Biological; D011401:Promoter Regions, Genetic / Q000235:genetics; D012042:Registries